Bromine in the structure of Crystal Structure of An Rna Tertiary Domain Essential to Hcv Ires-Mediated Translation Initiation. (pdb 1kh6)

The binding sites of Bromine atom in the structure of Crystal Structure of An Rna Tertiary Domain Essential to Hcv Ires-Mediated Translation Initiation. (pdb code 1kh6). This binding sites where shown with 5.0 Angstroms radius around Bromine atom. The 1kh6 structure was solved by J.S.KIEFT, K.ZHOU, A.GRECH, R JUBIN, J.A.DOUDNA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:

Resolution (A)

50.0-2.9

Space group

P42212

a (A)

66.532

b (A)

66.532

c (A)

95.850

alpha (°)

90.00

beta (°)

90.00

gamma (°)

90.00

Rfactor (%)

28.3

Rfree (%)

27.9

Bromine Binding Sites:

Bromine binding site 1 out of 6 in 1kh6

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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Bromine in the PDB 1kh6. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Bromine atom, shown by VdW sphereResidues shown as a stick model or VDW spheres: A: 5bu16,

conact list:

Atom

Atom

Distance (A)

Br

N3 A:5bu16

3.86

Br

C2 A:5bu16

4.42

Br

C6 A:5bu16

2.55

Br

N1 A:5bu16

3.85

Br

C5 A:5bu16

1.60

Br

O4' A:5bu16

4.97

Br

C4 A:5bu16

2.63

Br

BR A:5bu16

0.00

Br

O4 A:5bu16

2.98

interactive model:

Bromine binding site 2 out of 6 in 1kh6

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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Bromine in the PDB 1kh6. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Bromine atom, shown by VdW sphereResidues shown as a stick model or VDW spheres: A: A25, A: 5bu26, A: C27,

conact list:

Atom

Atom

Distance (A)

Br

N9 A:A25

3.90

Br

C3' A:A25

3.57

Br

C8 A:A25

3.59

Br

C5 A:A25

4.37

Br

C1' A:A25

4.41

Br

P A:A25

4.79

Br

N7 A:A25

3.92

Br

O3' A:A25

4.28

Br

O4' A:A25

4.79

Br

C4 A:A25

4.37

Br

OP2 A:A25

4.38

Br

C5' A:A25

4.83

Br

C2' A:A25

3.97

Br

C4' A:A25

4.63

Br

O5' A:A25

3.92

Br

N3 A:5bu26

3.85

Br

C2 A:5bu26

4.40

Br

C6 A:5bu26

2.55

Br

N1 A:5bu26

3.84

Br

C5 A:5bu26

1.61

Br

P A:5bu26

4.05

Br

O4' A:5bu26

4.92

Br

C4 A:5bu26

2.63

Br

OP2 A:5bu26

3.11

Br

BR A:5bu26

0.00

Br

O5' A:5bu26

4.02

Br

O4 A:5bu26

3.00

Br

C5 A:C27

4.64

Br

C4 A:C27

4.78

Br

N4 A:C27

4.19

interactive model:

Bromine binding site 3 out of 6 in 1kh6

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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Bromine in the PDB 1kh6. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Bromine atom, shown by VdW sphereResidues shown as a stick model or VDW spheres: A: A35, A: 5bu36, A: 5bu37,

conact list:

Atom

Atom

Distance (A)

Br

N9 A:A35

3.92

Br

N3 A:A35

4.93

Br

C3' A:A35

4.07

Br

C8 A:A35

3.63

Br

C6 A:A35

4.70

Br

C5 A:A35

3.97

Br

C1' A:A35

4.62

Br

N7 A:A35

3.68

Br

O3' A:A35

4.79

Br

C4 A:A35

4.13

Br

C2' A:A35

4.27

Br

O5' A:A35

4.73

Br

N3 A:5bu36

3.83

Br

C2 A:5bu36

4.39

Br

C6 A:5bu36

2.54

Br

N1 A:5bu36

3.84

Br

C5 A:5bu36

1.58

Br

P A:5bu36

4.44

Br

C4 A:5bu36

2.59

Br

OP2 A:5bu36

3.39

Br

BR A:5bu36

0.00

Br

O5' A:5bu36

4.41

Br

O4 A:5bu36

2.92

Br

BR A:5bu37

4.32

Br

O4 A:5bu37

4.93

interactive model:

Bromine binding site 4 out of 6 in 1kh6

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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Bromine in the PDB 1kh6. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Bromine atom, shown by VdW sphereResidues shown as a stick model or VDW spheres: A: 5bu36, A: 5bu37,

conact list:

Atom

Atom

Distance (A)

Br

N3 A:5bu36

4.14

Br

C3' A:5bu36

4.21

Br

C2 A:5bu36

4.25

Br

C6 A:5bu36

3.79

Br

N1 A:5bu36

4.04

Br

C5 A:5bu36

3.73

Br

C1' A:5bu36

4.80

Br

O2 A:5bu36

4.98

Br

O3' A:5bu36

4.90

Br

C4 A:5bu36

3.93

Br

C2' A:5bu36

4.41

Br

BR A:5bu36

4.32

Br

O5' A:5bu36

4.76

Br

O4 A:5bu36

4.43

Br

N3 A:5bu37

3.84

Br

C2 A:5bu37

4.40

Br

C6 A:5bu37

2.55

Br

N1 A:5bu37

3.85

Br

C5 A:5bu37

1.59

Br

P A:5bu37

4.50

Br

C4 A:5bu37

2.61

Br

OP2 A:5bu37

3.40

Br

BR A:5bu37

0.00

Br

O5' A:5bu37

4.49

Br

O4 A:5bu37

2.96

interactive model:

Bromine binding site 5 out of 6 in 1kh6

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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Bromine in the PDB 1kh6. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Bromine atom, shown by VdW sphereResidues shown as a stick model or VDW spheres: A: A24, A: 5bu37, A: 5bu38,

conact list:

Atom

Atom

Distance (A)

Br

C2 A:A24

4.92

Br

N1 A:A24

4.96

Br

N3 A:5bu37

4.01

Br

C3' A:5bu37

4.72

Br

C2 A:5bu37

3.65

Br

C6 A:5bu37

4.92

Br

N1 A:5bu37

4.18

Br

C1' A:5bu37

4.53

Br

O2 A:5bu37

3.51

Br

C4 A:5bu37

4.80

Br

C2' A:5bu37

3.80

Br

O2' A:5bu37

4.45

Br

N3 A:5bu38

3.87

Br

C2 A:5bu38

4.43

Br

C6 A:5bu38

2.58

Br

N1 A:5bu38

3.88

Br

C5 A:5bu38

1.61

Br

C4 A:5bu38

2.64

Br

OP2 A:5bu38

4.01

Br

BR A:5bu38

0.00

Br

O4 A:5bu38

3.00

interactive model:

Bromine binding site 6 out of 6 in 1kh6

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Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Bromine in the PDB 1kh6. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Bromine atom, shown by VdW sphereResidues shown as a stick model or VDW spheres: A: 5bu44,